Background: The gastrointestinal tract is the primary site of interaction
between the host immune system and microorganisms.
Studies have suggested that selective microbial targets may influence
the development of the allergic diseases. But the difference
in functional gene composition remains unknown. We aim to assess
the structural and functional gene composition of stool
microbiota of infants with eczema and their matched (for age,
gender, mode of delivery, feeding) controls at the age of 1
month.
Methods: Twelve children with eczema and their controls were
selected from the placebo arm of a birth cohort of at-risk infants participating
in a randomized double-blind trial on the protective effects
of supplemental probiotics in early life on allergic outcomes. The four
were caesarean delivery followed by formula feeding (eczema = 2
and healthy control = 2) and the eight were vaginal delivery followed
by partial breast feeding mixed with formula feeding (eczema = 4
and healthy control = 4). Bacterial genomic DNA were extracted from
fecal samples and prepared for Illumina Miseq and Hiseq sequencing.
Data analysis such as sequence quality check, contigs assembly and
gene annotation were carried out for the DNA sequences obtained
from Miseq and Hiseq sequencing.
Results: Phylogenetic analysis of metagenomic sequences revealed
that four phyla dominated both microbial communities: Proteobacteria
(54% and 63% for healthy and eczema communities, respectively),
Firmicutes (26% and 18%), Actinobacteria (13% and 8%),
Bacteroidetes (7% and 8%). Comparative metagenomic analysis
showed that immune-regulatory TCAAGCTTGA motifs were significantly
enriched in healthy communities, many of which were
encoded by Bifidobacterium (38% of the total motifs in the healthy
communities). Draft genomes of five Bifidobacterium species (B.
longum, B. bifidum, B. breve, B. dentium, and B. pseudocatenulatum )
were recovered from metagenomic datasets. The B. longum BFN-121-
2 genome encoded more TCAAGCTTGA motifs (4.2 copies per 1
million genome sequence) than other Bifidobacterium genomes and
was significantly overrepresented (P < 0.05) in the healthy
communities.
Conclusions: Our results report distinct immune-modulatory genomic
properties of gut microbiotas in healthy infants as compared to children
with eczema and provide new insights into potential roles of
gut microbiotas in affecting human immune homeostasis.

Background: The gastrointestinal tract is the primary site of interaction
between the host immune system and microorganisms.
Studies have suggested that selective microbial targets may influence
the development of the allergic diseases. But the difference
in functional gene composition remains unknown. We aim to assess
the structural and functional gene composition of stool
microbiota of infants with eczema and their matched (for age,
gender, mode of delivery, feeding) controls at the age of 1
month.
Methods: Twelve children with eczema and their controls were
selected from the placebo arm of a birth cohort of at-risk infants participating
in a randomized double-blind trial on the protective effects
of supplemental probiotics in early life on allergic outcomes. The four
were caesarean delivery followed by formula feeding (eczema = 2
and healthy control = 2) and the eight were vaginal delivery followed
by partial breast feeding mixed with formula feeding (eczema = 4
and healthy control = 4). Bacterial genomic DNA were extracted from
fecal samples and prepared for Illumina Miseq and Hiseq sequencing.
Data analysis such as sequence quality check, contigs assembly and
gene annotation were carried out for the DNA sequences obtained
from Miseq and Hiseq sequencing.
Results: Phylogenetic analysis of metagenomic sequences revealed
that four phyla dominated both microbial communities: Proteobacteria
(54% and 63% for healthy and eczema communities, respectively),
Firmicutes (26% and 18%), Actinobacteria (13% and 8%),
Bacteroidetes (7% and 8%). Comparative metagenomic analysis
showed that immune-regulatory TCAAGCTTGA motifs were significantly
enriched in healthy communities, many of which were
encoded by Bifidobacterium (38% of the total motifs in the healthy
communities). Draft genomes of five Bifidobacterium species (B.
longum, B. bifidum, B. breve, B. dentium, and B. pseudocatenulatum )
were recovered from metagenomic datasets. The B. longum BFN-121-
2 genome encoded more TCAAGCTTGA motifs (4.2 copies per 1
million genome sequence) than other Bifidobacterium genomes and
was significantly overrepresented (P < 0.05) in the healthy
communities.
Conclusions: Our results report distinct immune-modulatory genomic
properties of gut microbiotas in healthy infants as compared to children
with eczema and provide new insights into potential roles of
gut microbiotas in affecting human immune homeostasis.